BN1865 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.1648e-05 1.2195e-04
Layer 5 4.6733e-05 5.6076e-04
Layer 6 5.6263e-04 2.0865e-03
Layer 3 6.3256e-04 1.7084e-02
Layer 1 9.8912e-04 1.3089e-01
Layer 2 1.9832e-03 7.7318e-02
WM 5.4780e-03 1.5133e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
PRKAR1B Expression Distribution
Gene Specificity Score (GSS)
PRKAR1B GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
PRKAR1B Layer 4 3.2148 0.7158
SYT1 Layer 6 3.6836 0.7086
SULT4A1 Layer 4 2.9863 0.7081
STXBP1 Layer 4 3.0684 0.7069
STMN1 Layer 4 3.1523 0.7051
UCHL1 Layer 6 3.2891 0.7033
SNCA Layer 6 3.1523 0.7028
TAGLN3 Layer 4 2.8584 0.6937
DNM1 Layer 4 3.3105 0.6904
NCDN Layer 4 3.0059 0.6903
EEF1A2 Layer 5 3.2285 0.6903
ARL6IP1 Layer 5 2.7910 0.6891
SNAP91 Layer 6 2.9414 0.6871
RAB3A Layer 6 2.9219 0.6870
STMN2 Layer 5 3.4316 0.6828
SYN1 Layer 4 2.9805 0.6820
MEF2C Layer 4 3.2461 0.6820
YWHAH Layer 6 3.3252 0.6817
SYN2 Layer 6 3.2051 0.6813
SYP Layer 4 2.8770 0.6804
YWHAG Layer 6 3.1250 0.6802
INPP5F Layer 4 2.8223 0.6791
ZNF483 Layer 4 2.8652 0.6786
SYNGR3 Layer 5 2.2930 0.6772
ENO2 Layer 6 2.9277 0.6760
FAIM2 Layer 4 2.7852 0.6737
TBR1 Layer 6 2.7754 0.6734
BASP1 Layer 6 3.0488 0.6714
CLSTN1 Layer 6 2.9082 0.6713
NSF Layer 6 2.9053 0.6708
HPCA Layer 4 3.2363 0.6708
VSNL1 Layer 6 3.2422 0.6702
AGAP3 Layer 6 2.9277 0.6690
RTN1 Layer 6 3.5059 0.6684
NAPB Layer 6 3.2852 0.6678
SERPINI1 Layer 4 3.1191 0.6675
HPCAL4 Layer 6 2.6982 0.6667
SNRPN Layer 4 3.1602 0.6643
ITPK1 Layer 4 2.5176 0.6639
CELF4 Layer 4 2.5723 0.6626
ATP1B1 Layer 6 3.0781 0.6621
AUXG01000058.1 Layer 4 3.0361 0.6618
CALM3 Layer 6 3.0059 0.6611
MTURN Layer 4 2.5449 0.6606
TUBB4A Layer 6 2.8311 0.6599
NUDT4 Layer 4 2.8086 0.6595
SOD2 Layer 6 2.7539 0.6587
GAS7 Layer 4 2.5449 0.6584
ATP6V1B2 Layer 6 2.6426 0.6584
WDR82 Layer 4 2.5664 0.6583

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1865
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1865_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1865/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1865/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1865/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1865/report/PD/BN1865_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1865/report/PD/BN1865_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 09:13:51
  • Number of Processes: 10
  • Spending Time: 0h 3m